Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021471.1 Corchorus olitorius cultivar O-4 contig21504, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 40469
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Found at i:1965 original size:18 final size:20
Alignment explanation
Indices: 1935--1980 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
1925 TAAATAAATC
1935 ATTT-CTTTGACTTATTA-G
1 ATTTCCTTTGACTTATTATG
1953 ATTTCCTTT-ACTTATTATG
1 ATTTCCTTTGACTTATTATG
1972 -TTTCCTTTG
1 ATTTCCTTTG
1981 TTTCTTTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.17, C:0.15, G:0.09, T:0.59
Consensus pattern (20 bp):
ATTTCCTTTGACTTATTATG
Found at i:5892 original size:13 final size:13
Alignment explanation
Indices: 5876--5901 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5866 AATTAAATTG
5876 GAAAAAAGAAAAA
1 GAAAAAAGAAAAA
5889 GAAAAAAGAAAAA
1 GAAAAAAGAAAAA
5902 TTAAAGTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
GAAAAAAGAAAAA
Found at i:9868 original size:30 final size:30
Alignment explanation
Indices: 9832--9900 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
9822 ATCAAGCAAC
*
9832 CAAAGGTCCTGCACAA-GCCACTGCACCAAG
1 CAAAGGTCCTACA-AACGCCACTGCACCAAG
*
9862 CAAAGGTCCTACAAACTCCACTGCACCAAG
1 CAAAGGTCCTACAAACGCCACTGCACCAAG
9892 CAAAGGTCC
1 CAAAGGTCC
9901 ACCAAGGAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 2 0.06
30 34 0.94
ACGTcount: A:0.35, C:0.36, G:0.17, T:0.12
Consensus pattern (30 bp):
CAAAGGTCCTACAAACGCCACTGCACCAAG
Found at i:10433 original size:33 final size:33
Alignment explanation
Indices: 10361--10440 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
10351 AGATTTTTAC
* * *
10361 AAATGTAAAAATTAGGTGATAGTAGATTTCTGG
1 AAATGTTAACATTAGGTGATAGAAGATTTCTGG
* *
10394 AAATGTTAACATTAGGTGATGGAAGATTTCTGT
1 AAATGTTAACATTAGGTGATAGAAGATTTCTGG
10427 AAATGTTAACATTA
1 AAATGTTAACATTA
10441 ACATTAGATG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.35
Consensus pattern (33 bp):
AAATGTTAACATTAGGTGATAGAAGATTTCTGG
Found at i:10715 original size:16 final size:15
Alignment explanation
Indices: 10677--10718 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
10667 ACAGAGATTG
*
10677 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
10692 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
10707 ACTAGAAAACAA
1 AC-AGAAAACAA
10719 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:17847 original size:21 final size:21
Alignment explanation
Indices: 17821--17880 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
17811 GGAATGGCGA
17821 TGGCACGGGCATGGCCGATGG
1 TGGCACGGGCATGGCCGATGG
* ** *
17842 TGGCACGGGCTTAACCGGTGG
1 TGGCACGGGCATGGCCGATGG
*
17863 TGGCACGGTGAATGGCCG
1 TGGCACGG-GCATGGCCG
17881 GTAATGACTT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.15, C:0.23, G:0.45, T:0.17
Consensus pattern (21 bp):
TGGCACGGGCATGGCCGATGG
Found at i:21021 original size:15 final size:15
Alignment explanation
Indices: 20984--21026 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
20974 GTAAAAGTTC
*
20984 TTAAACAAAATTAAAA
1 TTAAAGAAAA-TAAAA
21000 TTAAAGACAAATAAAA
1 TTAAAGA-AAATAAAA
21016 -TAAAGAAAATA
1 TTAAAGAAAATA
21027 TATATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 5 0.20
15 6 0.24
16 11 0.44
17 3 0.12
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.21
Consensus pattern (15 bp):
TTAAAGAAAATAAAA
Found at i:21090 original size:26 final size:27
Alignment explanation
Indices: 21061--21125 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 27
21051 GAACAAGAAA
*
21061 TTTTTTTTATTTATGACGCATAAA-TT
1 TTTTTTTTATTTATGACGCAAAAACTT
**
21087 TTTTTTTTAAATATGACGCAAAAACTT
1 TTTTTTTTATTTATGACGCAAAAACTT
21114 TTTTTTTT-TTTA
1 TTTTTTTTATTTA
21126 AAAACGGCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 23 0.70
27 10 0.30
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58
Consensus pattern (27 bp):
TTTTTTTTATTTATGACGCAAAAACTT
Found at i:21542 original size:16 final size:15
Alignment explanation
Indices: 21504--21545 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
21494 ACAAAGGTTG
* *
21504 ACAGAAAATAATTGA
1 ACAGAAAACAATTAA
21519 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
21534 ACTAGAAAACAA
1 AC-AGAAAACAA
21546 AGTAGAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.64, C:0.12, G:0.10, T:0.14
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:24165 original size:12 final size:11
Alignment explanation
Indices: 24144--24197 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
24134 TCTCCTTTTA
24144 TTTTCTTTTCT
1 TTTTCTTTTCT
24155 TTTTCCTTTTCCAT
1 TTTT-CTTTT-C-T
24169 TTTT-TTTTCT
1 TTTTCTTTTCT
24179 TTTT-TTCTTCT
1 TTTTCTT-TTCT
24190 TTTT-TTTT
1 TTTTCTTTT
24198 ATGTTGGGCG
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.23
11 15 0.38
12 9 0.23
13 1 0.03
14 5 0.13
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:24176 original size:24 final size:22
Alignment explanation
Indices: 24136--24182 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 22
24126 GGGTTAGATC
24136 TCCTTTTATTTTCTTTTCTTTT
1 TCCTTTTATTTTCTTTTCTTTT
*
24158 TCCTTTTCCATTTTTTTTTCTTTT
1 TCCTTTT--ATTTTCTTTTCTTTT
24182 T
1 T
24183 TTCTTCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.32
24 15 0.68
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (22 bp):
TCCTTTTATTTTCTTTTCTTTT
Found at i:24189 original size:11 final size:10
Alignment explanation
Indices: 24139--24197 Score: 55
Period size: 10 Copynumber: 5.4 Consensus size: 10
24129 TTAGATCTCC
* *
24139 TTTTATTTTC
1 TTTTCTTTTT
24149 TTTTCTTTTT
1 TTTTCTTTTT
24159 CCTTTTCCATTTTT
1 --TTTT-C-TTTTT
24173 TTTTCTTTTT
1 TTTTCTTTTT
24183 TTCTTCTTTTT
1 TT-TTCTTTTT
24194 TTTT
1 TTTT
24198 ATGTTGGGCG
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
10 17 0.40
11 11 0.26
12 8 0.19
13 1 0.02
14 5 0.12
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:25917 original size:2 final size:2
Alignment explanation
Indices: 25910--25944 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
25900 CCATTATTAC
25910 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25945 GCTTTCACGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26063 original size:23 final size:22
Alignment explanation
Indices: 25993--26100 Score: 89
Period size: 22 Copynumber: 5.0 Consensus size: 22
25983 TTGAATTTTT
*
25993 TATGAAATTTTGATAA-CTACCC
1 TATGAAATTTTGATAACCT-TCC
* ****
26015 TATTAAATTTTGATAACCAAGT
1 TATGAAATTTTGATAACCTTCC
26037 TATGAAATTTTGATAAACCTTCC
1 TATGAAATTTTGAT-AACCTTCC
*
26060 TATGAAATTTTG-TAATC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
26080 TATG-ATTTTTGATAACATTCC
1 TATGAAATTTTGATAACCTTCC
26101 CTGTGAGATT
Statistics
Matches: 68, Mismatches: 14, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
19 6 0.09
20 10 0.15
21 6 0.09
22 29 0.43
23 17 0.25
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:26112 original size:42 final size:44
Alignment explanation
Indices: 26044--26138 Score: 115
Period size: 42 Copynumber: 2.2 Consensus size: 44
26034 AGTTATGAAA
* *
26044 TTTTGATAAACCTTCCTATGAAATTTTG-TAATCTC-CTATGA-T
1 TTTTGAT-AACATTCCTATGAAATTTTGTTAATCTCTCTATAATT
* *
26086 TTTTGATAACATTCCCTGTGAGATTTTGTTAATCTCTCTATAATT
1 TTTTGATAACATT-CCTATGAAATTTTGTTAATCTCTCTATAATT
26131 TTTTGATA
1 TTTTGATA
26139 CTATAGTATG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
41 5 0.11
42 19 0.42
43 7 0.16
44 5 0.11
45 9 0.20
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (44 bp):
TTTTGATAACATTCCTATGAAATTTTGTTAATCTCTCTATAATT
Found at i:28028 original size:2 final size:2
Alignment explanation
Indices: 28021--28051 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28011 GTAGTTAGAA
28021 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28052 ATACTTTGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29185 original size:33 final size:33
Alignment explanation
Indices: 29148--29227 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
29138 GCCTGCGCAG
*
29148 GCGCCTGGCCAGCGCTGCGGGCCACACTGGCCT
1 GCGCCTGGCCAGCGCTGCGGGCCACACAGGCCT
29181 GCGCCTGGCCAGCGCTGCGGGCCACACAGGCCT
1 GCGCCTGGCCAGCGCTGCGGGCCACACAGGCCT
*
29214 TCGCGCTAGGCCAG
1 GCGC-CT-GGCCAG
29228 GCAGCCGCGC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
33 35 0.81
34 2 0.05
35 6 0.14
ACGTcount: A:0.11, C:0.41, G:0.36, T:0.11
Consensus pattern (33 bp):
GCGCCTGGCCAGCGCTGCGGGCCACACAGGCCT
Found at i:29404 original size:13 final size:14
Alignment explanation
Indices: 29380--29420 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
29370 CCCAAGCCAG
29380 AAAGAGAAAAGAAGA
1 AAAGA-AAAAGAAGA
29395 AAA-AAAAAGAAGA
1 AAAGAAAAAGAAGA
29408 AAAGGAAAAAGAA
1 AAA-GAAAAAGAA
29421 AAAGGAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
15 11 0.46
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAGAAGA
Found at i:29450 original size:21 final size:21
Alignment explanation
Indices: 29378--29450 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
29368 GGCCCAAGCC
* *
29378 AGAAAGAGAAAAGAA-G-AAA
1 AGAAAAAGAAAATAAGGAAAA
29397 A-AAAAAGAAGAA-AAGGAAAA
1 AGAAAAAGAA-AATAAGGAAAA
* *
29417 AGAAAAAGGAAATAAGGAATA
1 AGAAAAAGAAAATAAGGAAAA
29438 AGATAAAA-AAAAT
1 AGA-AAAAGAAAAT
29451 GGAAAATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
18 9 0.20
19 4 0.09
20 6 0.14
21 21 0.48
22 4 0.09
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (21 bp):
AGAAAAAGAAAATAAGGAAAA
Found at i:31799 original size:21 final size:22
Alignment explanation
Indices: 31752--31798 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
31742 GCAATTTTCT
*
31752 TTTTTAAAAAAAGTAATGGCAA
1 TTTTAAAAAAAAGTAATGGCAA
31774 TTTTAAAAAAAAGTAATGGCAA
1 TTTTAAAAAAAAGTAATGGCAA
31796 TTT
1 TTT
31799 AGAAATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.34
Consensus pattern (22 bp):
TTTTAAAAAAAAGTAATGGCAA
Found at i:32449 original size:27 final size:26
Alignment explanation
Indices: 32400--32451 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 26
32390 TTTCTATCAT
32400 TTTAATAATGGAATAATTAAAATATTA
1 TTTAATAATGGAAT-ATTAAAATATTA
32427 TTTAATAATGGCAAT-TTAGAAATAT
1 TTTAATAATGG-AATATTA-AAATAT
32452 ATTAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 3 0.13
27 17 0.74
28 3 0.13
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (26 bp):
TTTAATAATGGAATATTAAAATATTA
Found at i:34140 original size:25 final size:26
Alignment explanation
Indices: 34097--34146 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
34087 GGTACTGTAC
34097 AAATTGAATTTTTCTAAATAAAATAA
1 AAATTGAATTTTTCTAAATAAAATAA
34123 AAATTGAA-TTTTCTAAATAAAATA
1 AAATTGAATTTTTCTAAATAAAATA
34147 TTTTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (26 bp):
AAATTGAATTTTTCTAAATAAAATAA
Found at i:34330 original size:25 final size:27
Alignment explanation
Indices: 34278--34343 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
34268 AAAAGTACAC
*
34278 AAAATTATATTTTAATAGTGGCATAA-TT
1 AAAA-TATATTTTAATAATGGCA-AATTT
*
34306 AAAATATTTTTTAATAATGGC-AATTT
1 AAAATATATTTTAATAATGGCAAATTT
34332 AGAAATATATTT
1 A-AAATATATTT
34344 GGAGAAAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 2 0.06
26 3 0.09
27 24 0.73
28 4 0.12
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (27 bp):
AAAATATATTTTAATAATGGCAAATTT
Found at i:36660 original size:95 final size:95
Alignment explanation
Indices: 36497--36689 Score: 350
Period size: 95 Copynumber: 2.0 Consensus size: 95
36487 ATTTTACTCA
*
36497 TTGACATTATAGTATGTTCAATAATGAAACCAATAAGTTTGATCTTGTGTTTTTCCCTTGTAAGA
1 TTGACATTATAGTAGGTTCAATAATGAAACCAATAAGTTTGATCTTGTGTTTTTCCCTTGTAAGA
36562 AAAGACAAGTGATGTGAATGTCTGCCTTGT
66 AAAGACAAGTGATGTGAATGTCTGCCTTGT
*
36592 TTGACATTTTAGTAGGTTCAATAATGAAACCAATAAGTTTGATCTTGTGTTTTTCCCTTGTAAGA
1 TTGACATTATAGTAGGTTCAATAATGAAACCAATAAGTTTGATCTTGTGTTTTTCCCTTGTAAGA
* *
36657 AAAGACAAGTGATGTGAATGTTTGCGTTGT
66 AAAGACAAGTGATGTGAATGTCTGCCTTGT
36687 TTG
1 TTG
36690 CTTTGGTTGT
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (95 bp):
TTGACATTATAGTAGGTTCAATAATGAAACCAATAAGTTTGATCTTGTGTTTTTCCCTTGTAAGA
AAAGACAAGTGATGTGAATGTCTGCCTTGT
Done.